You need to add the full app path to the WSGIPythonPath Directive in apache's config. The reason your app is not a valid python module is because it is not located on the python path. What makes something a valid python module basically is "a directory on the python path with an init.py file in it".

It is normal for the path configuration requirements to be different between projects and to be configured upon deployment. Also depending on how old the other stacks are they might just have different default configuration.